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The regulatory landscape controlling Hoxd gene expression in tetrapod digit development was probably co-opted from a pre-existing cloacal regulatory mechanism, as evidenced by the effects of genetic deletion experiments in zebrafish fin, cloaca and mouse urogenital development.

The authors discovered cluster of regulatory sequences that controls HOXA over large genomic distances and across topological domains. This cluster is required for normal craniofacial development in both humans and mice.

The organization of Hox clusters in several different reptiles is investigated, showing that the Hox clusters in squamates — lizards and snakes — have unexpectedly accumulated transposable elements, reflecting extensive genomic rearrangements of coding and non coding regulatory regions. Comparative expression analyses between two species showing different axial skeletons, the corn snake and the whiptail lizard, revealed major alterations in Hox13 and Hox10 expression features during snake somitogenesis, in line with the expansion of both caudal and thoracic regions.

The HOX gene cluster is responsible for anteroposterior axis patterning in an evolutionarily conserved manner. Here they examine HOX gene expression in human embryos and show that neural-crest derivatives retain the anatomical HOX code of their origin while also adopting the code of their destination.

Mice evolved a new shape in the upper, but not in the lower molar. In addition to developmental changes specific to the upper molar, this occurred through shared changes with the lower molar, the development of which has drifted to support upper molar adaptation.

The basic five-digit limb of tetrapods has been altered many times during evolution, usually by the progressive loss of digits — this study tracks the molecular underpinnings of this change, showing that in comparison to mouse, the polarized gene expression in the bovine limb bud is progressively lost due to evolutionary alteration of the cis-regulatory sequences that control Ptch1 expression in response to SHH signalling in the digit-forming handplate.

Approximately a quarter of the human genome consists of gene deserts. Here, Abassah-Oppong et al. reveal the biological relevance, embryonic functions and underlying enhancer architecture of a genomic gene desert flanking the Shox2 transcription factor essential for limb, craniofacial and cardiac pacemaker development.

CTCF is as an architectural protein involved in 3D genome folding; however its contribution to animal development has not been well characterized. Here the authors show that CTCF is not only pivotal for 3D chromatin structure and enhancer-promoter interactions in zebrafish, but it is also essential for controlling the expression of thousands of genes during development.

Genomic, epigenomic and transcriptomic data derived from the Mediterranean amphioxus (Branchiostoma lanceolatum) provide insights into the evolution of the genomic regulatory landscape of chordates.

The developing mouse gut endoderm, mapped at single-cell resolution, reveals trajectories of cell differentiation before and during gastrulation and the emergence of regionalized cell identities along the anterior–posterior axis of the gut tube.

How are the complex and varied roles of retinoic acid orchestrated at multiple developmental stages? Recent studies have highlighted the importance of tightly regulating its distribution, of switching the activities of its nuclear receptors, and of interactions with other key developmental signalling molecules.

How left–right asymmetries are established in vertebrate embryos has fascinated developmental biologists for decades. Recent evidence from a range of species provides insights into the genetic and epigenetic mechanisms that are involved, particularly in the early stages of generating left–right asymmetry.

The European Mouse Mutagenesis Consortium is the European initiative contributing to the international effort on functional annotation of the mouse genome. Its objectives are to establish and integrate mutagenesis platforms, gene expression resources, phenotyping units, storage and distribution centers and bioinformatics resources. The combined efforts will accelerate our understanding of gene function and of human health and disease.

There are now myriad variations on techniques to reprogramme somatic cells into pluripotent stem cells, but which options should researchers choose? This Review sets out the choices, focusing on how the desired downstream application should guide the reprogramming strategy.